The reef system is currently suffering an invasion by the red lionfish (Pterois volitans and Pterois miles), which is native to the Indo-Pacific region. Lionfish severely damage the reef ecosystem by eating nearly every reef-tending species, such as cleaner shrimp and other species that eat algae. These animals keep the corals clean, alive, and disease-free. Lionfish eat up to 90% of the reef-tending species in a given area within just a few months, which can result in a quick death for a reef. Valuable commercial species, such as lobster, are being negatively affected by the spread of the lionfish due to the enormous appetite of the invasive lionfish.

The reef system is home to one of the world's largest populations of manatees, with an estimated 1,000 to 1,500 of them.[2]

Some northern areas of the reef system near Isla Contoy are home to the largest fish on the planet, the whale shark.[2] The normally solitary whale sharks congregate there in social groups to eat and to mate.